2011 May
- BQGB 090528 – Berkeley Quantitative Genome Browser
- DNAmend 1.02a – Create Virtual DNA Constructs
- genePI 20080506 – Gene promoter identification system
- PriorsEditor 1.0.11 – Create and use Positional Priors in Motif Discovery
- JAMIE 0.91 – Joint Analysis of Multiple ChIP-chip Experiments
- TileMap v2 – Tiling Array Peak Detection
- CisGenome 2.0 – ChIP-chip and ChIP-seq Data Analysis
- VEMS 5.18042011 – Analysis of MS-based Proteomics Data
- SNPYGoat 1.0 – Identify Several Goat Y-chromosomal Haplotypes
- HapYDive – Excel Plugin for Y-STR Haplotype Diversity Calculation
- DNAux 3.0 – Generate Random DNA Sequences & Compute Overlapped Sequence
- RepeatAround 2.1 – Find Repeats in Circular Genomes
- LocalMotif 1.0 – Discover Transcription Factor Binding Motifs
- AssociationViewer 2.0 – Display SNPs in Genetic Context
- Ameliorator 1.0 – Calculate Amelioration Times for DNA Sequence Evolution
- RNAFold – Create Batch files for the FOLD module of the GCG
- Spector II – Calculate Concentration of Oligonucleotides based on OD Values
- Genetic Code – Show the Universal Genetic Code
- Jack the Knife 1.0 – Estimate the Significance of Traits
- DNA Master 5.22.1 – DNA sequence editor and analysis package
- goldMINER 2.0.27 – Use CDD to Automate Sequence Annotation
- YCDMA 3.1.1 – Manage Microsatellite Data
- WinIPaup 1.0 – Windows Interface for PAUP to Create NEXUS Files
- NSA 3.3 – Nucleotide Sequence Analyzer
- Xplorer 2.4.2 – Chromatogram Editor with Mutation Detection
- DNA Counter 1.0.2 – Caculate Proportions of A,C G, T ,CG, AT in DNA Sequence
- PlantDB 2.01 – Database for Managing Plant Research
- EVE v04 – Detect Differentially Expressed Genes using Microarray Data
- WinPep 3.01 – Analysis of Aminoacid Sequences
- WinGene 2.31 – Analysis of Nucleotide Sequences
- MB 6.84 – DNA Analysis Program
- iCE 3.5 – View Fingerprint Maps & Associated Data
- GenomeComp 1.3 – Whole Genome Compare & Visulization Tool
- GenescanView 1.2 – Visualize Genescan Files
- GenomePixelizer 2003.10.1 – Genome Visualization Tool
- MeltCalc 2.0 – Thermodynamic Probe Design
- GDA 1.1 – Analyze Discrete Population Genetic Data
- DNAPlotter 1.4 – Circular & Linear Interactive Genome Visualisation
- DNA for Windows 2.51 – DNA Sequence Editing & Analysis Program
- VariScan 2.0.3 – Analysis of DNA Sequence Polymorphisms at the Whole Genome-scale
- MANVa 0.982b – Multilocus Analysis of Nucleotide Variation
- mlcoalsim 1.42 – Multilocus Coalescent Simulations
- DnaSP 5.10.01 – Analysis of Nucleotide Polymorphism from Aligned DNA Sequence Data
- OpenMM Zephyr 2.0.3 – Molecular Simulation Application
- COSMOS 5.0 / COSMOS Viewer 3.0 – Computer Simulation & Visualisation of Molecular Structures
- OpenAstexViewer 3.0 – Software for Molecular Visualisation
- APSC 1.0 – Convert Protein Sequence File Format
- Autodock/Vina plugin for PyMOL
- PyRx 0.8 – Virtual Screening software for Computer-Aided Drug Design
- AutoDock Vina 1.1.2 – Molecular Docking and Virtual Screening Program
- ChemSpotlight 2.0 – Plugin of MacOsX Spotlight for Reading Chemical Files
- Zodiac 0.6.5 – Molecular Modelling suite for Drug Design
- PDB Editor 090203 – PDB (Protein Data Bank) File Editor
- ProteinShader beta 0.9.4 – Illustrative Rendering of Macromolecules
- BioEditor 1.6.1 – Present Macromolecular Structure & Structural Annotation
- NOC 3.01 – Molecular Explorer for Protein Structure Visualization
- ProteinScope 1.0.5 – 3D Protein Structure Viewer
- Ramachandran Plot Explorer 1.0 – Interactive Cross-platform Protein Viewer
- Protein Explorer 2.80 – Visualize 3D Structures of Macromolecules
- PULCHRA 3.06 – All-atom Reconstruction & Refinement of Reduced Protein Models
- CCOMP 3.70 – Compare Ligand/Receptor Complexes
- iMol 0.40 – Molecular Visualization Application for Mac OS X
- Biodesigner 0.75 – Molecular Modeling & Visualization
- JMVS 4 041122 – Java3D Molecular Visualisation System
- StrukEd – Editor for Molecules & 3D Viewer
- AUTOGSCAN 1.03 – Automated Genome-wide Linkage & Linkage Disequilibrium Analysis
- Analyze – Collection of Linkage & Assosiation software
- Vocabulon 1.0 – Identification of Conserved Words in DNA Sequence
- MicroMerge 2.0 – Merge Microsatellite Genotype Data Sets
- GSearcher 1.4 – Cytoscape Plugin for Searching over Complex Attribute Tables
- Filo 1.1 – Simulate Sequence Data used in Phylogenetic Analyses
- CoSpec – Show Coevolutionary Behaviours of Two Phylogenies
- Spectrum 2.0 – Show Phylogenetic Information in a Data Set
- TreeMap 3.0b – Compare Host & Parasite Trees
- GNLab -Computational Pipeline for Large-Scale Gene Network Analysis
- VersaCount 1.02 / VersaCount Max! 0.6 – Assist with the Counting of Cells
- GRaPe 1.0 – Generation of Generic Rate Equations for all Reactions in a Model
- Utopia 1.4.5 – Protein Analysis Suite
- Arcadia 1.0rc2 – Visualisation Tool for Metabolic Pathways
- OrthoSelect – Selection of Orthologs in Phylogenomics
- Orphelia – Predict Genes in Metagenomic Sequencing Reads
- YACOP 2 – Gene Prediction for Prokaryotes
- TiCo 2.1 – Postprosessing of Gene Predictions for Prokaryotes
- Anchored DIALIGN 2.2.2 – Multiple Sequence Alignment with User-defined Constraints
- Treephyler 1.1 – Fast Taxonomic Profiling of Metagenomes.
- PLINK 1.07 – Whole Genome Association Analysis Toolset
- MapMaker 3 – Genetic Linkage Analysis & Mapping Genes Complex Traits
- LocusView 2.0 – Generate Images of Chromosomal Regions
- GENEHUNTER 2.1 – Multipoint Analysis of Pedigree Data
- Haploview 4.2 – Analysis & Visualization of LD & Haplotype Maps
- CYTOWIN 4.31 – Flow Cytometry Analysis Software
- MFI 3.4kb8 – Analysis of Flow Cytofluorometry Data
- LDATAPP 2.0 – Convert FCS data to ASCII text
- Cell Counter 3.2 – Count Cells
- Visual3D 1.2 – Generate 3D Visualization of Fluorescence Microscopy Images
- Deconvolve 2.1 – Remote Batch Restorations of 3D/2D Fluorescence Images
- RefreshRatio 4.0 – Refresh Ratios in Flow Cytometry List-Files
- ListMath 2.1 – Create Histograms & Plots from Flow Cytometry List-Files
- Flow Explorer 4.2 – Analysis for Flow Cytometry File
- FASPAD 20070415 – Detection of Linear Signaling Pathways in Protein Interaction Networks
- MetaPAT 20070215 – Tool for the Alignment of Metabolic Pathways
- Visualisation tools – Display 2-loop & 3-loop Arabidopsis Clock Models
- Brass 3.0 – Biological Rhythms Analysis Software System
- Circadian Modelling 2.0 – Simulations using Mathematical Models of Biological Clocks
- Bio-PEPA Workbench 1.0 – Bench of Language for the Modelling & the Analysis of Biochemical Networks
- XML2PDB – Extract PDB file from XML Structure File
- ProtBuD – Protein Biological Unit Database
- DashPDB – Mac OS X Dashboard widget to Access to the RCSB Protein Data Bank
- ArboDraw 2006 – Phylogenetic Tree Builder & Viewer
- MolIDE 1.7 – Protein 3D Homology Modeling
- SCWRL 4.0 – Prediction of Protein Side-chain Conformation
- BioDownloader 2.2.1.0- Download and/or Update Files from Servers
- DISTANCE – Plot Genetic Distances between Populations
- DESIRE 1.1 – Target your Genetic Gains
- GENUP 5.5 – Computer Aided Learning for Quantitative Genetics
- PEDIGREE VIEWER 6.5b – Draw & Manipulate Pedigree Diagrams
- Cyton Calculator – Reads CFSE data and Calculates Cyton Model Parameters
- Hackit – Program for Clipping & Joining FCS List Mode Data Files
- De-Identifier – Remove Patient Identification from FCS file
- Cellular Symphony – Audio Representation of Flow Cytometric Data
- MapDraw 2.1 – Excel Macro for Drawing Genetic Linkage Maps
- GemStone 1.0 – Analysis of High-dimensional, Flow Cytometry Data
- WinMDI 2.9 – Windows Multiple Document Interafce for Flow Cytometry
- LRASSOC 1.1 – Analysis of Case-control Data for Diseases with Two Susceptiblity Loci
- HAPSIM – Produce the Case-control Multilocus Genotype Data
- NNPERM 1.3 – Analyse Case-control Multi-locus Genotype Data
- TABLE 1.9 – Convert Output from Linkage Analysis to more Readable Form
- QUIKLINK 1.6 – Linkage Analyses with a Variety of Programs
- SDT 2.0 – multiallele SDT and TDT analysis
- QDB 2.6 – General Database Program suitable for Managing Genetic Data
- CHECKHET 1.0 – Detect Genetic Outliers in Case-control Samples
- SIBASS 1.4 – Association Test using Siblings as Controls
- COMBASSOC 1.3 – Overall Significance of Multiple analysis
- QMFLINK 1.1 – Model-free Linkage Analysis of Quantitative Traits
- MFLINK 3.4 – Model-free Linkage Analysis
- ETDT 2.5 – Multiallele TDT Analysis
- CLUMPHAP 1.1 – Haplotype-based Association Analysis
- CLUMP 2.4 – Assess Significance of Case-control Association Studies with Multi-allelic Markers
- MRVTEST 1.0 – Model-free Linkage Analysis using Likelihoods
- PEDRAW 2.5 – Pedigree Drawing Program
- PED 6.0.2 – Pedigree Drawing Software
- GEST98 – Analysis of Genotype x Environment Interaction
- DIAL98 – Diallel Analysis of Full & Half Diallel Tables
- MAPL98 – Linkage Mapping & QTL Analysis
- AcePerl 1.91 – Perl Interface for ACEDB database
- JADE 1.0j – Java for ACEDB
- SNP-HWE – Routines for exact SNP tests of Hardy-Weinberg Equilibrium
- PSEUDO 0.3.5 – Evaluate Empirical P-values for Linkage Scans
- FUGUE 0.2.3 – Haplotype Frequency Estimation
- Metal 20110325 – Meta-analysis of Genomewide Association Scans
- CaTS 0.0.2 – Power Calculator for Two Stage Association Studies
- PEDSTATS 0.6.12 – Statistics & Quality Assessments for Gene-mapping Data
- Haplotyper 1.0 – Genotype Format Data from an Excel File to a Format of Arlequin
- SimWalk 2.91 – Statistical Analysis of Qualitative Traits
- GOLD 1.1.0 – Graphical Overview of Linkage Disequilibrium
- QTDT 2.6.1 – Linkage Disequilibrium Analysis for Quantitative and Discrete Traits
- MACH 1.0 – Haplotyping, Genotype Imputation & Disease Association Analysis
- LAMP 0.0.9 – Linkage & Association Modeling for Pedigrees
- MERLIN 1.1.2 – Pedigree Analysis
- GRR 1.2.1.41 – Detect Pedigree Errors
- BOXIT 2007 – Database for Molecular Biology Laboratories
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